The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GenotypeGVCFs reporting every site to have MQ0=0
In the past, I’ve found MQ0 ("Total Mapping Quality Zero Reads") to be a very useful INFO feature of putatively variable sites. However, in my experience, GenotypeGVCFs reports every site to have MQ0=0, even those for which UnifiedGenotyper reports MQ0 > 0 when run on the same data. Is this a bug, or am I missing something?